1. Baseline Characteristics

1.1 With original MMRd types

?
(N=5)
Complex
(N=11)
MLH1_PMS2
(N=251)
MSH2_MSH6
(N=70)
MSH6
(N=12)
NORMAL
(N=19)
PMS2
(N=13)
Total
(N=381)
Age (years)
Mean (SD) 64.4 (12.8) 63.8 (19.9) 67.9 (13.2) 56.8 (14.1) 64.5 (11.2) 61.1 (14.5) 54.3 (16.7) 64.8 (14.4)
Median [Min, Max] 63.0 [46.0, 77.0] 70.0 [26.0, 88.0] 71.0 [25.0, 90.0] 55.0 [30.0, 90.0] 67.0 [36.0, 76.0] 65.0 [31.0, 87.0] 48.0 [37.0, 84.0] 67.0 [25.0, 90.0]
Race
BLACK OR AFRICAN AMERICAN 1 (20.0%) 0 (0%) 15 (6.0%) 4 (5.7%) 0 (0%) 1 (5.3%) 1 (7.7%) 22 (5.8%)
PT REFUSED TO ANSWER 1 (20.0%) 0 (0%) 6 (2.4%) 1 (1.4%) 0 (0%) 1 (5.3%) 0 (0%) 9 (2.4%)
WHITE 3 (60.0%) 8 (72.7%) 208 (82.9%) 57 (81.4%) 10 (83.3%) 16 (84.2%) 9 (69.2%) 311 (81.6%)
ASIAN-FAR EAST/INDIAN SUBCONT 0 (0%) 2 (18.2%) 11 (4.4%) 4 (5.7%) 1 (8.3%) 1 (5.3%) 3 (23.1%) 22 (5.8%)
OTHER 0 (0%) 1 (9.1%) 9 (3.6%) 4 (5.7%) 1 (8.3%) 0 (0%) 0 (0%) 15 (3.9%)
NATIVE AMERICAN-AM IND/ALASKA 0 (0%) 0 (0%) 2 (0.8%) 0 (0%) 0 (0%) 0 (0%) 0 (0%) 2 (0.5%)
Ethnicity
Non-Spanish; Non-Hispanic 5 (100%) 8 (72.7%) 215 (85.7%) 58 (82.9%) 11 (91.7%) 18 (94.7%) 11 (84.6%) 326 (85.6%)
"Spanish NOS; Hispanic NOS, Latino NOS" 0 (0%) 2 (18.2%) 14 (5.6%) 8 (11.4%) 1 (8.3%) 1 (5.3%) 1 (7.7%) 27 (7.1%)
Dominican Republic 0 (0%) 1 (9.1%) 0 (0%) 0 (0%) 0 (0%) 0 (0%) 0 (0%) 1 (0.3%)
0 0 (0%) 0 (0%) 3 (1.2%) 2 (2.9%) 0 (0%) 0 (0%) 0 (0%) 5 (1.3%)
Puerto Rican 0 (0%) 0 (0%) 2 (0.8%) 0 (0%) 0 (0%) 0 (0%) 0 (0%) 2 (0.5%)
Unknown whether Spanish or not 0 (0%) 0 (0%) 17 (6.8%) 2 (2.9%) 0 (0%) 0 (0%) 1 (7.7%) 20 (5.2%)
Tumor Purity (%)
Mean (SD) 48.0 (19.2) 38.2 (12.7) 38.3 (16.0) 39.6 (15.8) 39.6 (16.3) 47.2 (17.0) 38.8 (19.4) 39.2 (16.1)
Median [Min, Max] 50.0 [20.0, 70.0] 30.0 [25.0, 60.0] 40.0 [10.0, 90.0] 40.0 [5.00, 80.0] 30.0 [25.0, 80.0] 50.0 [20.0, 70.0] 35.0 [10.0, 70.0] 40.0 [5.00, 90.0]
Missing 0 (0%) 0 (0%) 1 (0.4%) 2 (2.9%) 0 (0%) 0 (0%) 0 (0%) 3 (0.8%)
Cancer Type
Bladder 1 (20.0%) 0 (0%) 0 (0%) 5 (7.1%) 2 (16.7%) 0 (0%) 1 (7.7%) 9 (2.4%)
Endometrial 1 (20.0%) 1 (9.1%) 62 (24.7%) 14 (20.0%) 1 (8.3%) 4 (21.1%) 0 (0%) 83 (21.8%)
Esophagogastric 2 (40.0%) 1 (9.1%) 33 (13.1%) 4 (5.7%) 0 (0%) 2 (10.5%) 0 (0%) 42 (11.0%)
Small Bowel 1 (20.0%) 0 (0%) 4 (1.6%) 2 (2.9%) 0 (0%) 1 (5.3%) 4 (30.8%) 12 (3.1%)
Colon 0 (0%) 9 (81.8%) 118 (47.0%) 19 (27.1%) 4 (33.3%) 7 (36.8%) 4 (30.8%) 161 (42.3%)
Biliary 0 (0%) 0 (0%) 5 (2.0%) 0 (0%) 0 (0%) 0 (0%) 1 (7.7%) 6 (1.6%)
Colorectal 0 (0%) 0 (0%) 10 (4.0%) 5 (7.1%) 3 (25.0%) 4 (21.1%) 1 (7.7%) 23 (6.0%)
CUP 0 (0%) 0 (0%) 5 (2.0%) 0 (0%) 0 (0%) 1 (5.3%) 0 (0%) 6 (1.6%)
Other 0 (0%) 0 (0%) 2 (0.8%) 5 (7.1%) 0 (0%) 0 (0%) 0 (0%) 7 (1.8%)
Ovarian 0 (0%) 0 (0%) 1 (0.4%) 2 (2.9%) 0 (0%) 0 (0%) 1 (7.7%) 4 (1.0%)
Pancreas 0 (0%) 0 (0%) 1 (0.4%) 2 (2.9%) 1 (8.3%) 0 (0%) 0 (0%) 4 (1.0%)
Prostate 0 (0%) 0 (0%) 1 (0.4%) 2 (2.9%) 1 (8.3%) 0 (0%) 0 (0%) 4 (1.0%)
Rectal 0 (0%) 0 (0%) 9 (3.6%) 10 (14.3%) 0 (0%) 0 (0%) 1 (7.7%) 20 (5.2%)
Sample Type
Metastasis 1 (20.0%) 1 (9.1%) 29 (11.6%) 6 (8.6%) 2 (16.7%) 4 (21.1%) 2 (15.4%) 45 (11.8%)
Mixed 1 (20.0%) 1 (9.1%) 17 (6.8%) 5 (7.1%) 2 (16.7%) 1 (5.3%) 1 (7.7%) 28 (7.3%)
Primary 3 (60.0%) 9 (81.8%) 205 (81.7%) 59 (84.3%) 8 (66.7%) 14 (73.7%) 10 (76.9%) 308 (80.8%)

1.2 With MMRd types collapsed by Multiplex or not

Singleton
(N=25)
?
(N=5)
Multiplex
(N=332)
NORMAL
(N=19)
Total
(N=381)
Age (years)
Mean (SD) 59.2 (15.0) 64.4 (12.8) 65.4 (14.3) 61.1 (14.5) 64.8 (14.4)
Median [Min, Max] 64.0 [36.0, 84.0] 63.0 [46.0, 77.0] 68.0 [25.0, 90.0] 65.0 [31.0, 87.0] 67.0 [25.0, 90.0]
Race
ASIAN-FAR EAST/INDIAN SUBCONT 4 (16.0%) 0 (0%) 17 (5.1%) 1 (5.3%) 22 (5.8%)
BLACK OR AFRICAN AMERICAN 1 (4.0%) 1 (20.0%) 19 (5.7%) 1 (5.3%) 22 (5.8%)
OTHER 1 (4.0%) 0 (0%) 14 (4.2%) 0 (0%) 15 (3.9%)
WHITE 19 (76.0%) 3 (60.0%) 273 (82.2%) 16 (84.2%) 311 (81.6%)
PT REFUSED TO ANSWER 0 (0%) 1 (20.0%) 7 (2.1%) 1 (5.3%) 9 (2.4%)
NATIVE AMERICAN-AM IND/ALASKA 0 (0%) 0 (0%) 2 (0.6%) 0 (0%) 2 (0.5%)
Ethnicity
"Spanish NOS; Hispanic NOS, Latino NOS" 2 (8.0%) 0 (0%) 24 (7.2%) 1 (5.3%) 27 (7.1%)
Non-Spanish; Non-Hispanic 22 (88.0%) 5 (100%) 281 (84.6%) 18 (94.7%) 326 (85.6%)
Unknown whether Spanish or not 1 (4.0%) 0 (0%) 19 (5.7%) 0 (0%) 20 (5.2%)
0 0 (0%) 0 (0%) 5 (1.5%) 0 (0%) 5 (1.3%)
Dominican Republic 0 (0%) 0 (0%) 1 (0.3%) 0 (0%) 1 (0.3%)
Puerto Rican 0 (0%) 0 (0%) 2 (0.6%) 0 (0%) 2 (0.5%)
Tumor Purity (%)
Mean (SD) 39.2 (17.6) 48.0 (19.2) 38.6 (15.8) 47.2 (17.0) 39.2 (16.1)
Median [Min, Max] 30.0 [10.0, 80.0] 50.0 [20.0, 70.0] 40.0 [5.00, 90.0] 50.0 [20.0, 70.0] 40.0 [5.00, 90.0]
Missing 0 (0%) 0 (0%) 3 (0.9%) 0 (0%) 3 (0.8%)
Cancer Type
Colon 8 (32.0%) 0 (0%) 146 (44.0%) 7 (36.8%) 161 (42.3%)
Biliary 1 (4.0%) 0 (0%) 5 (1.5%) 0 (0%) 6 (1.6%)
Bladder 3 (12.0%) 1 (20.0%) 5 (1.5%) 0 (0%) 9 (2.4%)
Colorectal 4 (16.0%) 0 (0%) 15 (4.5%) 4 (21.1%) 23 (6.0%)
CUP 0 (0%) 0 (0%) 5 (1.5%) 1 (5.3%) 6 (1.6%)
Endometrial 1 (4.0%) 1 (20.0%) 77 (23.2%) 4 (21.1%) 83 (21.8%)
Esophagogastric 0 (0%) 2 (40.0%) 38 (11.4%) 2 (10.5%) 42 (11.0%)
Other 0 (0%) 0 (0%) 7 (2.1%) 0 (0%) 7 (1.8%)
Ovarian 1 (4.0%) 0 (0%) 3 (0.9%) 0 (0%) 4 (1.0%)
Pancreas 1 (4.0%) 0 (0%) 3 (0.9%) 0 (0%) 4 (1.0%)
Prostate 1 (4.0%) 0 (0%) 3 (0.9%) 0 (0%) 4 (1.0%)
Rectal 1 (4.0%) 0 (0%) 19 (5.7%) 0 (0%) 20 (5.2%)
Small Bowel 4 (16.0%) 1 (20.0%) 6 (1.8%) 1 (5.3%) 12 (3.1%)
Sample Type
Metastasis 4 (16.0%) 1 (20.0%) 36 (10.8%) 4 (21.1%) 45 (11.8%)
Mixed 3 (12.0%) 1 (20.0%) 23 (6.9%) 1 (5.3%) 28 (7.3%)
Primary 18 (72.0%) 3 (60.0%) 273 (82.2%) 14 (73.7%) 308 (80.8%)

1.3 With MMRd types collapsed by MSH6 or not

MSH6
(N=82)
Not_MSH6
(N=299)
Total
(N=381)
Age (years)
Mean (SD) 57.9 (13.9) 66.6 (14.0) 64.8 (14.4)
Median [Min, Max] 56.5 [30.0, 90.0] 70.0 [25.0, 90.0] 67.0 [25.0, 90.0]
Race
ASIAN-FAR EAST/INDIAN SUBCONT 5 (6.1%) 17 (5.7%) 22 (5.8%)
BLACK OR AFRICAN AMERICAN 4 (4.9%) 18 (6.0%) 22 (5.8%)
OTHER 5 (6.1%) 10 (3.3%) 15 (3.9%)
PT REFUSED TO ANSWER 1 (1.2%) 8 (2.7%) 9 (2.4%)
WHITE 67 (81.7%) 244 (81.6%) 311 (81.6%)
NATIVE AMERICAN-AM IND/ALASKA 0 (0%) 2 (0.7%) 2 (0.5%)
Ethnicity
"Spanish NOS; Hispanic NOS, Latino NOS" 9 (11.0%) 18 (6.0%) 27 (7.1%)
0 2 (2.4%) 3 (1.0%) 5 (1.3%)
Non-Spanish; Non-Hispanic 69 (84.1%) 257 (86.0%) 326 (85.6%)
Unknown whether Spanish or not 2 (2.4%) 18 (6.0%) 20 (5.2%)
Dominican Republic 0 (0%) 1 (0.3%) 1 (0.3%)
Puerto Rican 0 (0%) 2 (0.7%) 2 (0.5%)
Tumor Purity (%)
Mean (SD) 39.6 (15.8) 39.1 (16.2) 39.2 (16.1)
Median [Min, Max] 40.0 [5.00, 80.0] 40.0 [10.0, 90.0] 40.0 [5.00, 90.0]
Missing 2 (2.4%) 1 (0.3%) 3 (0.8%)
Cancer Type
Colon 23 (28.0%) 138 (46.2%) 161 (42.3%)
Biliary 0 (0%) 6 (2.0%) 6 (1.6%)
Bladder 7 (8.5%) 2 (0.7%) 9 (2.4%)
Colorectal 8 (9.8%) 15 (5.0%) 23 (6.0%)
CUP 0 (0%) 6 (2.0%) 6 (1.6%)
Endometrial 15 (18.3%) 68 (22.7%) 83 (21.8%)
Esophagogastric 4 (4.9%) 38 (12.7%) 42 (11.0%)
Other 5 (6.1%) 2 (0.7%) 7 (1.8%)
Ovarian 2 (2.4%) 2 (0.7%) 4 (1.0%)
Pancreas 3 (3.7%) 1 (0.3%) 4 (1.0%)
Prostate 3 (3.7%) 1 (0.3%) 4 (1.0%)
Rectal 10 (12.2%) 10 (3.3%) 20 (5.2%)
Small Bowel 2 (2.4%) 10 (3.3%) 12 (3.1%)
Sample Type
Metastasis 8 (9.8%) 37 (12.4%) 45 (11.8%)
Mixed 7 (8.5%) 21 (7.0%) 28 (7.3%)
Primary 67 (81.7%) 241 (80.6%) 308 (80.8%)

1.4With MMRd types collapsed by PMS2 or not

PMS2
(N=264)
Not_PMS2
(N=117)
Total
(N=381)
Age (years)
Mean (SD) 67.2 (13.7) 59.3 (14.6) 64.8 (14.4)
Median [Min, Max] 70.0 [25.0, 90.0] 59.0 [26.0, 90.0] 67.0 [25.0, 90.0]
Race
ASIAN-FAR EAST/INDIAN SUBCONT 14 (5.3%) 8 (6.8%) 22 (5.8%)
BLACK OR AFRICAN AMERICAN 16 (6.1%) 6 (5.1%) 22 (5.8%)
NATIVE AMERICAN-AM IND/ALASKA 2 (0.8%) 0 (0%) 2 (0.5%)
OTHER 9 (3.4%) 6 (5.1%) 15 (3.9%)
PT REFUSED TO ANSWER 6 (2.3%) 3 (2.6%) 9 (2.4%)
WHITE 217 (82.2%) 94 (80.3%) 311 (81.6%)
Ethnicity
"Spanish NOS; Hispanic NOS, Latino NOS" 15 (5.7%) 12 (10.3%) 27 (7.1%)
0 3 (1.1%) 2 (1.7%) 5 (1.3%)
Non-Spanish; Non-Hispanic 226 (85.6%) 100 (85.5%) 326 (85.6%)
Puerto Rican 2 (0.8%) 0 (0%) 2 (0.5%)
Unknown whether Spanish or not 18 (6.8%) 2 (1.7%) 20 (5.2%)
Dominican Republic 0 (0%) 1 (0.9%) 1 (0.3%)
Tumor Purity (%)
Mean (SD) 38.3 (16.1) 41.1 (16.0) 39.2 (16.1)
Median [Min, Max] 40.0 [10.0, 90.0] 40.0 [5.00, 80.0] 40.0 [5.00, 90.0]
Missing 1 (0.4%) 2 (1.7%) 3 (0.8%)
Cancer Type
Colon 122 (46.2%) 39 (33.3%) 161 (42.3%)
Biliary 6 (2.3%) 0 (0%) 6 (1.6%)
Bladder 1 (0.4%) 8 (6.8%) 9 (2.4%)
Colorectal 11 (4.2%) 12 (10.3%) 23 (6.0%)
CUP 5 (1.9%) 1 (0.9%) 6 (1.6%)
Endometrial 62 (23.5%) 21 (17.9%) 83 (21.8%)
Esophagogastric 33 (12.5%) 9 (7.7%) 42 (11.0%)
Other 2 (0.8%) 5 (4.3%) 7 (1.8%)
Ovarian 2 (0.8%) 2 (1.7%) 4 (1.0%)
Pancreas 1 (0.4%) 3 (2.6%) 4 (1.0%)
Prostate 1 (0.4%) 3 (2.6%) 4 (1.0%)
Rectal 10 (3.8%) 10 (8.5%) 20 (5.2%)
Small Bowel 8 (3.0%) 4 (3.4%) 12 (3.1%)
Sample Type
Metastasis 31 (11.7%) 14 (12.0%) 45 (11.8%)
Mixed 18 (6.8%) 10 (8.5%) 28 (7.3%)
Primary 215 (81.4%) 93 (79.5%) 308 (80.8%)

2. Linear Mixed Effect Regression Model to predict the genomic features with original MMRd types

Apply a statistical model to predict genomic features with multiple fixed effects,

MMRd Types, Cancer Types, Age, Tumor purity, Race and more, adjusting for random effects like Metastatic status

#####Groups: Complex, MSH2_MSH6, MLH1_PMS2, MSH6, PMS2, Normal

#####Formula: Feautre ~ MMRd.Type +/* Cancer.Type + Age + Tumor.purity + Race + (1 + MMRd.Type | Metastatic.status)

3. Linear Mixed Effect Regression Model to predict the genomic features with collapsed MMRd types

Apply a statistical model to predict genomic features with multiple fixed effects,

MMRd Types(collapsed), Cancer Types, Age, Tumor purity, Race and more, adjusting for random effects like Metastatic status

3.1 Significances By collapsed Multiplex or not

#####Groups: 1) Singleton: MSH6, PMS2; 2) Multiplex: MSH2_MSH6, MLH1_PMS2, Complex; 3) Normal;

#####Formula: Feautre ~ Multiplex_or_not +/* Cancer.Type + Age + Tumor.purity + Race + (1 + Multiplex_or_not | Metastatic.status)

3.2 Significances By collapsed MSH6 or not

#####Groups: 1) MSH6: MSH2_MSH6, MSH6; 2) Not_MSH6: MLH1_PMS2, PMS2, Normal

#####Formula: Feautre ~ MSH6_or_not +/* Cancer.Type + Age + Tumor.purity + Race + (1 + MSH6_or_not | Metastatic.status)

3.3 Significances By collapsed PMS2 or not

#####Groups: 1) PMS2: MLH1_PMS2, PMS2; 2) Not_PMS2: MSH2_MSH6, MSH6, Normal

Feautre ~ PMS2_or_not +/* Cancer.Type + Age + Tumor.purity + Race + (1 + PMS2_or_not | Metastatic.status)

4. Survival Plots with all MMRd and Cancer types

  • 4.1 Plot OS difference between original/collapsed MMRd types (e.g.: Multiplex vs Singleton; MSH6 vs Non_MSH6; PMS2 vs Non_PMS2), across all or most populated cancer types (e.g. “Colon”, “Endometrial”, “Esophagogastric”)
  • 4.2 Plot OS difference between Y/N of oncogenic mutations in the genes (e.g.: TP53, KRAS, BRAF, RNF43)

5 Aneuploidy Analysis

Aneuploidy Score Background 1 Aneuploidy Score Background 2

6. Luiz permbro-treated WES Data

6.1 Baseline Characteristics

MSH2_MSH6
(N=9)
MLH1_PMS2
(N=9)
PMS2
(N=1)
MSH6
(N=2)
?
(N=7)
Total
(N=28)
Age
Mean (SD) 50.6 (16.1) 50.4 (11.9) 50.0 (NA) 53.5 (2.12) 53.4 (9.80) 51.4 (11.9)
Median [Min, Max] 57.0 [29.0, 71.0] 52.0 [24.0, 64.0] 50.0 [50.0, 50.0] 53.5 [52.0, 55.0] 52.0 [39.0, 67.0] 52.0 [24.0, 71.0]
Gender
Female 2 (22.2%) 4 (44.4%) 0 (0%) 0 (0%) 5 (71.4%) 11 (39.3%)
Male 7 (77.8%) 5 (55.6%) 1 (100%) 2 (100%) 2 (28.6%) 17 (60.7%)
Race
Asian 1 (11.1%) 0 (0%) 0 (0%) 0 (0%) 0 (0%) 1 (3.6%)
White 8 (88.9%) 8 (88.9%) 1 (100%) 2 (100%) 5 (71.4%) 24 (85.7%)
Unknown 0 (0%) 1 (11.1%) 0 (0%) 0 (0%) 0 (0%) 1 (3.6%)
Black or African American 0 (0%) 0 (0%) 0 (0%) 0 (0%) 2 (28.6%) 2 (7.1%)
Ethnicity
non-Hispanic 9 (100%) 7 (77.8%) 1 (100%) 2 (100%) 7 (100%) 26 (92.9%)
Hispanic 0 (0%) 2 (22.2%) 0 (0%) 0 (0%) 0 (0%) 2 (7.1%)
Lynch.Clinical
No 1 (11.1%) 4 (44.4%) 0 (0%) 0 (0%) 2 (28.6%) 7 (25.0%)
UNK 0 (0%) 1 (11.1%) 0 (0%) 0 (0%) 1 (14.3%) 2 (7.1%)
Yes 8 (88.9%) 4 (44.4%) 1 (100%) 2 (100%) 4 (57.1%) 19 (67.9%)
TumorType
Ampulla of Vater 2 (22.2%) 0 (0%) 0 (0%) 1 (50.0%) 0 (0%) 3 (10.7%)
Cholangiocarcinoma 1 (11.1%) 0 (0%) 0 (0%) 0 (0%) 0 (0%) 1 (3.6%)
Colorectal 3 (33.3%) 7 (77.8%) 0 (0%) 0 (0%) 5 (71.4%) 15 (53.6%)
Endometrial cancer 1 (11.1%) 1 (11.1%) 0 (0%) 0 (0%) 2 (28.6%) 4 (14.3%)
Gastroesophageal cancer 1 (11.1%) 0 (0%) 1 (100%) 0 (0%) 0 (0%) 2 (7.1%)
Small Intestine 1 (11.1%) 1 (11.1%) 0 (0%) 0 (0%) 0 (0%) 2 (7.1%)
Thyroid 0 (0%) 0 (0%) 0 (0%) 1 (50.0%) 0 (0%) 1 (3.6%)
Assembly
hg18 7 (77.8%) 5 (55.6%) 0 (0%) 1 (50.0%) 5 (71.4%) 18 (64.3%)
hg19 2 (22.2%) 4 (44.4%) 1 (100%) 1 (50.0%) 2 (28.6%) 10 (35.7%)

6.2 Genomic Feature Exploration

MSH2_MSH6
MLH1_PMS2
PMS2
MSH6
Overall
PD
(N=4)
SD
(N=1)
PR
(N=1)
CR
(N=3)
PD
(N=1)
SD
(N=2)
PR
(N=4)
CR
(N=2)
PD
(N=1)
NE
(N=2)
NE
(N=2)
PD
(N=6)
SD
(N=3)
PR
(N=5)
CR
(N=5)
Stop_variant
Mean (SD) 0 (0) 0 (NA) 0 (NA) 0 (0) 0 (NA) 0 (0) 0 (0) 0 (0) 1.00 (NA) 0 (0) 0 (0) 0.167 (0.408) 0 (0) 0 (0) 0 (0)
Median [Min, Max] 0 [0, 0] 0 [0, 0] 0 [0, 0] 0 [0, 0] 0 [0, 0] 0 [0, 0] 0 [0, 0] 0 [0, 0] 1.00 [1.00, 1.00] 0 [0, 0] 0 [0, 0] 0 [0, 1.00] 0 [0, 0] 0 [0, 0] 0 [0, 0]
Start_variant
Mean (SD) 0 (0) 1.00 (NA) 0 (NA) 0 (0) 0 (NA) 0.500 (0.707) 0 (0) 0 (0) 0 (NA) 0 (0) 0 (0) 0 (0) 0.667 (0.577) 0 (0) 0 (0)
Median [Min, Max] 0 [0, 0] 1.00 [1.00, 1.00] 0 [0, 0] 0 [0, 0] 0 [0, 0] 0.500 [0, 1.00] 0 [0, 0] 0 [0, 0] 0 [0, 0] 0 [0, 0] 0 [0, 0] 0 [0, 0] 1.00 [0, 1.00] 0 [0, 0] 0 [0, 0]
Splice_site_donor
Mean (SD) 22.5 (11.8) 88.0 (NA) 11.0 (NA) 89.3 (72.5) 6.00 (NA) 23.5 (21.9) 36.0 (7.87) 25.0 (5.66) 22.0 (NA) 24.5 (0.707) 24.5 (0.707) 19.7 (11.3) 45.0 (40.3) 31.0 (13.1) 63.6 (62.3)
Median [Min, Max] 27.5 [5.00, 30.0] 88.0 [88.0, 88.0] 11.0 [11.0, 11.0] 49.0 [46.0, 173] 6.00 [6.00, 6.00] 23.5 [8.00, 39.0] 36.5 [26.0, 45.0] 25.0 [21.0, 29.0] 22.0 [22.0, 22.0] 24.5 [24.0, 25.0] 24.5 [24.0, 25.0] 24.0 [5.00, 30.0] 39.0 [8.00, 88.0] 35.0 [11.0, 45.0] 46.0 [21.0, 173]
Splice_site_acceptor
Mean (SD) 103 (68.1) 22.0 (NA) 33.0 (NA) 202 (5.86) 11.0 (NA) 80.0 (103) 152 (34.2) 119 (4.95) 24.0 (NA) 68.5 (50.2) 68.5 (50.2) 74.7 (69.0) 60.7 (80.3) 128 (60.7) 169 (46.2)
Median [Min, Max] 129 [5.00, 151] 22.0 [22.0, 22.0] 33.0 [33.0, 33.0] 200 [198, 209] 11.0 [11.0, 11.0] 80.0 [7.00, 153] 155 [110, 186] 119 [115, 122] 24.0 [24.0, 24.0] 68.5 [33.0, 104] 68.5 [33.0, 104] 67.0 [5.00, 151] 22.0 [7.00, 153] 138 [33.0, 186] 198 [115, 209]
Nonsynonymous_coding
Mean (SD) 845 (423) 3240 (NA) 203 (NA) 2100 (1230) 374 (NA) 1950 (1300) 720 (199) 574 (120) 1260 (NA) 1360 (757) 1360 (757) 835 (431) 2380 (1180) 616 (288) 1490 (1210)
Median [Min, Max] 728 [472, 1450] 3240 [3240, 3240] 203 [203, 203] 1410 [1360, 3520] 374 [374, 374] 1950 [1030, 2870] 746 [455, 932] 574 [489, 658] 1260 [1260, 1260] 1360 [820, 1890] 1360 [820, 1890] 728 [374, 1450] 2870 [1030, 3240] 710 [203, 932] 1360 [489, 3520]
Nonsense
Mean (SD) 45.8 (31.1) 65.0 (NA) 10.0 (NA) 88.7 (15.8) 20.0 (NA) 47.0 (32.5) 35.5 (14.2) 36.0 (18.4) 53.0 (NA) 67.0 (49.5) 67.0 (49.5) 42.7 (26.7) 53.0 (25.2) 30.4 (16.8) 67.6 (32.3)
Median [Min, Max] 37.0 [19.0, 90.0] 65.0 [65.0, 65.0] 10.0 [10.0, 10.0] 85.0 [75.0, 106] 20.0 [20.0, 20.0] 47.0 [24.0, 70.0] 34.0 [20.0, 54.0] 36.0 [23.0, 49.0] 53.0 [53.0, 53.0] 67.0 [32.0, 102] 67.0 [32.0, 102] 37.0 [19.0, 90.0] 65.0 [24.0, 70.0] 31.0 [10.0, 54.0] 75.0 [23.0, 106]
Inframe_Ins
Mean (SD) 2.00 (2.71) 1.00 (NA) 0 (NA) 7.33 (2.52) 1.00 (NA) 7.50 (2.12) 3.50 (0.577) 4.00 (0) 1.00 (NA) 1.00 (1.41) 1.00 (1.41) 1.67 (2.16) 5.33 (4.04) 2.80 (1.64) 6.00 (2.55)
Median [Min, Max] 1.00 [0, 6.00] 1.00 [1.00, 1.00] 0 [0, 0] 7.00 [5.00, 10.0] 1.00 [1.00, 1.00] 7.50 [6.00, 9.00] 3.50 [3.00, 4.00] 4.00 [4.00, 4.00] 1.00 [1.00, 1.00] 1.00 [0, 2.00] 1.00 [0, 2.00] 1.00 [0, 6.00] 6.00 [1.00, 9.00] 3.00 [0, 4.00] 5.00 [4.00, 10.0]
Inframe_Del
Mean (SD) 14.0 (11.3) 5.00 (NA) 5.00 (NA) 30.3 (2.52) 9.00 (NA) 23.0 (15.6) 20.8 (6.24) 20.5 (0.707) 17.0 (NA) 4.00 (1.41) 4.00 (1.41) 13.7 (9.16) 17.0 (15.1) 17.6 (8.88) 26.4 (5.68)
Median [Min, Max] 10.5 [5.00, 30.0] 5.00 [5.00, 5.00] 5.00 [5.00, 5.00] 30.0 [28.0, 33.0] 9.00 [9.00, 9.00] 23.0 [12.0, 34.0] 21.0 [14.0, 27.0] 20.5 [20.0, 21.0] 17.0 [17.0, 17.0] 4.00 [3.00, 5.00] 4.00 [3.00, 5.00] 11.5 [5.00, 30.0] 12.0 [5.00, 34.0] 17.0 [5.00, 27.0] 28.0 [20.0, 33.0]
Frameshift
Mean (SD) 267 (131) 537 (NA) 105 (NA) 578 (75.6) 179 (NA) 273 (326) 388 (96.1) 293 (45.3) 536 (NA) 102 (91.2) 102 (91.2) 297 (159) 361 (276) 331 (151) 464 (167)
Median [Min, Max] 278 [125, 386] 537 [537, 537] 105 [105, 105] 621 [491, 623] 179 [179, 179] 273 [42.0, 503] 394 [273, 489] 293 [261, 325] 536 [536, 536] 102 [37.0, 166] 102 [37.0, 166] 278 [125, 536] 503 [42.0, 537] 348 [105, 489] 491 [261, 623]
NE
PD
SD
PR
CR
Overall
MSH6
(N=2)
MSH2_MSH6
(N=4)
MLH1_PMS2
(N=1)
PMS2
(N=1)
MSH2_MSH6
(N=1)
MLH1_PMS2
(N=2)
MSH2_MSH6
(N=1)
MLH1_PMS2
(N=4)
MSH2_MSH6
(N=3)
MLH1_PMS2
(N=2)
MSH2_MSH6
(N=9)
MLH1_PMS2
(N=9)
PMS2
(N=1)
MSH6
(N=2)
Stop_variant
Mean (SD) 0 (0) 0 (0) 0 (NA) 1.00 (NA) 0 (NA) 0 (0) 0 (NA) 0 (0) 0 (0) 0 (0) 0 (0) 0 (0) 1.00 (NA) 0 (0)
Median [Min, Max] 0 [0, 0] 0 [0, 0] 0 [0, 0] 1.00 [1.00, 1.00] 0 [0, 0] 0 [0, 0] 0 [0, 0] 0 [0, 0] 0 [0, 0] 0 [0, 0] 0 [0, 0] 0 [0, 0] 1.00 [1.00, 1.00] 0 [0, 0]
Start_variant
Mean (SD) 0 (0) 0 (0) 0 (NA) 0 (NA) 1.00 (NA) 0.500 (0.707) 0 (NA) 0 (0) 0 (0) 0 (0) 0.111 (0.333) 0.111 (0.333) 0 (NA) 0 (0)
Median [Min, Max] 0 [0, 0] 0 [0, 0] 0 [0, 0] 0 [0, 0] 1.00 [1.00, 1.00] 0.500 [0, 1.00] 0 [0, 0] 0 [0, 0] 0 [0, 0] 0 [0, 0] 0 [0, 1.00] 0 [0, 1.00] 0 [0, 0] 0 [0, 0]
Splice_site_donor
Mean (SD) 24.5 (0.707) 22.5 (11.8) 6.00 (NA) 22.0 (NA) 88.0 (NA) 23.5 (21.9) 11.0 (NA) 36.0 (7.87) 89.3 (72.5) 25.0 (5.66) 50.8 (51.9) 27.4 (13.7) 22.0 (NA) 24.5 (0.707)
Median [Min, Max] 24.5 [24.0, 25.0] 27.5 [5.00, 30.0] 6.00 [6.00, 6.00] 22.0 [22.0, 22.0] 88.0 [88.0, 88.0] 23.5 [8.00, 39.0] 11.0 [11.0, 11.0] 36.5 [26.0, 45.0] 49.0 [46.0, 173] 25.0 [21.0, 29.0] 30.0 [5.00, 173] 29.0 [6.00, 45.0] 22.0 [22.0, 22.0] 24.5 [24.0, 25.0]
Splice_site_acceptor
Mean (SD) 68.5 (50.2) 103 (68.1) 11.0 (NA) 24.0 (NA) 22.0 (NA) 80.0 (103) 33.0 (NA) 152 (34.2) 202 (5.86) 119 (4.95) 119 (81.1) 113 (64.0) 24.0 (NA) 68.5 (50.2)
Median [Min, Max] 68.5 [33.0, 104] 129 [5.00, 151] 11.0 [11.0, 11.0] 24.0 [24.0, 24.0] 22.0 [22.0, 22.0] 80.0 [7.00, 153] 33.0 [33.0, 33.0] 155 [110, 186] 200 [198, 209] 119 [115, 122] 147 [5.00, 209] 122 [7.00, 186] 24.0 [24.0, 24.0] 68.5 [33.0, 104]
Nonsynonymous_coding
Mean (SD) 1360 (757) 845 (423) 374 (NA) 1260 (NA) 3240 (NA) 1950 (1300) 203 (NA) 720 (199) 2100 (1230) 574 (120) 1460 (1170) 923 (763) 1260 (NA) 1360 (757)
Median [Min, Max] 1360 [820, 1890] 728 [472, 1450] 374 [374, 374] 1260 [1260, 1260] 3240 [3240, 3240] 1950 [1030, 2870] 203 [203, 203] 746 [455, 932] 1410 [1360, 3520] 574 [489, 658] 1360 [203, 3520] 710 [374, 2870] 1260 [1260, 1260] 1360 [820, 1890]
Nonsense
Mean (SD) 67.0 (49.5) 45.8 (31.1) 20.0 (NA) 53.0 (NA) 65.0 (NA) 47.0 (32.5) 10.0 (NA) 35.5 (14.2) 88.7 (15.8) 36.0 (18.4) 58.2 (33.9) 36.4 (17.7) 53.0 (NA) 67.0 (49.5)
Median [Min, Max] 67.0 [32.0, 102] 37.0 [19.0, 90.0] 20.0 [20.0, 20.0] 53.0 [53.0, 53.0] 65.0 [65.0, 65.0] 47.0 [24.0, 70.0] 10.0 [10.0, 10.0] 34.0 [20.0, 54.0] 85.0 [75.0, 106] 36.0 [23.0, 49.0] 65.0 [10.0, 106] 31.0 [20.0, 70.0] 53.0 [53.0, 53.0] 67.0 [32.0, 102]
Inframe_Ins
Mean (SD) 1.00 (1.41) 2.00 (2.71) 1.00 (NA) 1.00 (NA) 1.00 (NA) 7.50 (2.12) 0 (NA) 3.50 (0.577) 7.33 (2.52) 4.00 (0) 3.44 (3.64) 4.22 (2.22) 1.00 (NA) 1.00 (1.41)
Median [Min, Max] 1.00 [0, 2.00] 1.00 [0, 6.00] 1.00 [1.00, 1.00] 1.00 [1.00, 1.00] 1.00 [1.00, 1.00] 7.50 [6.00, 9.00] 0 [0, 0] 3.50 [3.00, 4.00] 7.00 [5.00, 10.0] 4.00 [4.00, 4.00] 1.00 [0, 10.0] 4.00 [1.00, 9.00] 1.00 [1.00, 1.00] 1.00 [0, 2.00]
Inframe_Del
Mean (SD) 4.00 (1.41) 14.0 (11.3) 9.00 (NA) 17.0 (NA) 5.00 (NA) 23.0 (15.6) 5.00 (NA) 20.8 (6.24) 30.3 (2.52) 20.5 (0.707) 17.4 (12.5) 19.9 (7.91) 17.0 (NA) 4.00 (1.41)
Median [Min, Max] 4.00 [3.00, 5.00] 10.5 [5.00, 30.0] 9.00 [9.00, 9.00] 17.0 [17.0, 17.0] 5.00 [5.00, 5.00] 23.0 [12.0, 34.0] 5.00 [5.00, 5.00] 21.0 [14.0, 27.0] 30.0 [28.0, 33.0] 20.5 [20.0, 21.0] 14.0 [5.00, 33.0] 20.0 [9.00, 34.0] 17.0 [17.0, 17.0] 4.00 [3.00, 5.00]
Frameshift
Mean (SD) 102 (91.2) 267 (131) 179 (NA) 536 (NA) 537 (NA) 273 (326) 105 (NA) 388 (96.1) 578 (75.6) 293 (45.3) 383 (204) 318 (150) 536 (NA) 102 (91.2)
Median [Min, Max] 102 [37.0, 166] 278 [125, 386] 179 [179, 179] 536 [536, 536] 537 [537, 537] 273 [42.0, 503] 105 [105, 105] 394 [273, 489] 621 [491, 623] 293 [261, 325] 386 [105, 623] 325 [42.0, 503] 536 [536, 536] 102 [37.0, 166]

6.3 Mutation Signatures

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